Sorry, I started that branch a while ago, so it’s not compatible with the latest version of the stack (which you’re using). I’ve just now made the branch compatible with w_2018_11. You’ll need to git fetch && git reset --hard origin/tickets/DM-13148.
Let me know if you start using w_2018_12, as I’ll need to upgrade the branch again.
Thank you, Paul. That fixed it. I also had some issues specifying the mapper. Following the getting started tutorial, I run the command:
echo “lsst.obs.suprimecam.suprimecamMapper” > DATA/_mapper
and when I follow that up with:
ingestImages.py DATA $OBS_SUBARU_DIR/scam/raw/*.fits --mode=link
I get the following error:
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/bin/ingestImages.py", line 3, in <module>
IngestTask.parseAndRun()
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/ingest.py", line 396, in parseAndRun
args = parser.parse_args(config)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/argumentParser.py", line 566, in parse_args
mapperClass = dafPersist.Butler.getMapperClass(namespace.input)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butler.py", line 1135, in getMapperClass
return Storage.getMapperClass(root)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/storage.py", line 123, in getMapperClass
ret = Storage.storages[parseRes.scheme].getMapperClass(uri)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/posixStorage.py", line 216, in getMapperClass
pkg = importlib.import_module(".".join(components[:-1]))
File "/opt/lsst/software/stack/python/miniconda3-4.3.21/lib/python3.6/importlib/__init__.py", line 126, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 978, in _gcd_import
File "<frozen importlib._bootstrap>", line 961, in _find_and_load
File "<frozen importlib._bootstrap>", line 950, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 678, in exec_module
File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
File "/home/lsst/obs_subaru/python/lsst/obs/subaru/__init__.py", line 27, in <module>
from .version import *
ModuleNotFoundError: No module named 'lsst.obs.subaru.version'
This happens when trying to reduce data for both Suprimecam and HSC using obs_subaru. Do you have an idea of why? Thanks again, I really appreciate it!
You need to build your obs_subaru by running scons.
Notice also that SuprimecamMapper in your /path/to/DATA/_mapper file should have a leading capital S.
I was able to get the mapper set up and run ingestImages, but have been having trouble running ingestCalibs. Perhaps I am not using it correctly. I am receiving the error:
bash-4.2$ ingestCalibs.py DATA scam/CALIB/BIAS/*.fits --mode=link --validity 1000 --calibType bias
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/ingestCalibs.py'
CameraMapper INFO: Loading exposure registry from /home/lsst/DATA/registry.sqlite3
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/bin/ingestCalibs.py", line 3, in <module>
IngestCalibsTask.parseAndRun()
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/ingest.py", line 398, in parseAndRun
task.run(args)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/ingestCalibs.py", line 219, in run
with self.register.openRegistry(calibRoot, create=args.create, dryrun=args.dryrun) as registry:
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/ingestCalibs.py", line 86, in openRegistry
return RegisterTask.openRegistry(self, directory, create, dryrun, name)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/ingest.py", line 279, in openRegistry
registryName = os.path.join(directory, name)
File "/opt/lsst/software/stack/python/miniconda3-4.3.21/lib/python3.6/posixpath.py", line 78, in join
a = os.fspath(a)
TypeError: expected str, bytes or os.PathLike object, not NoneType
I believe the problem is happening in
"/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/ingestCalibs.py", line 217
though I am not 100% sure.
ingestCalibs.py works on “master” calibs created by our code. Unless you’ve run constructBias.py, you’re probably pointing at raw data (which should have been ingested with ingestImages.py) or a master calib created by different code which may not have the expected headers.
In any case, you didn’t specify a calibration directory (with --calib) in which to put the ingested calibs, which I suspect is the problem causing the TypeError.
I’m not sure I understand how to get the reference catalog working. Following these instructions, I have grabbed the appropriate FITS files (plus config.py and README.txt), and have installed them into my data repository using
ln -s scam/ps1_pv3_3pi_20170110/ DATA/ref_cats/. I’ve also adjusted my configuration, adding
from lsst.meas.algorithms import LoadIndexedReferenceObjectsTask
config.calibrate.astromRefObjLoader.retarget(LoadIndexedReferenceObjectsTask)
config.calibrate.astromRefObjLoader.ref_dataset_name = "ps1_pv3_3pi_20170110"
config.calibrate.photoRefObjLoader.retarget(LoadIndexedReferenceObjectsTask)
config.calibrate.photoRefObjLoader.ref_dataset_name = "ps1_pv3_3pi_20170110"
config.calibrate.photoCal.photoCatName = "ps1_pv3_3pi_20170110"
to the existing config/processCcd.py in the obs_subaru package (I have also tried specifying it with as a seperate file with --configfile). Biases and flats are constructed and ingested. When I run
processCcd.py DATA --rerun processCcdOutput --id, I get the error:
bash-4.2$ processCcd.py DATA --rerun processCcdOutput --id
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/processCcd.py'
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/suprimecam/processCcd.py'
CameraMapper INFO: Loading exposure registry from /home/lsst/DATA/registry.sqlite3
CameraMapper INFO: Loading calib registry from /home/lsst/DATA/CALIB/calibRegistry.sqlite3
root INFO: Running: /opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/bin/processCcd.py DATA --rerun processCcdOutput --id
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/bin/processCcd.py", line 25, in <module>
ProcessCcdTask.parseAndRun()
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 586, in parseAndRun
resultList = taskRunner.run(parsedCmd)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 233, in run
if self.precall(parsedCmd):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 347, in precall
task = self.makeTask(parsedCmd=parsedCmd)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 472, in makeTask
return self.TaskClass(config=self.config, log=self.log, butler=butler)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/processCcd.py", line 161, in __init__
astromRefObjLoader=astromRefObjLoader, photoRefObjLoader=photoRefObjLoader)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/task.py", line 299, in makeSubtask
subtask = taskField.apply(name=name, parentTask=self, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pex_config/14.0-4-gae1598d+1/python/lsst/pex/config/configurableField.py", line 83, in apply
return self.target(*args, config=self.value, **kw)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/calibrate.py", line 365, in __init__
self.makeSubtask('astromRefObjLoader', butler=butler)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/task.py", line 299, in makeSubtask
subtask = taskField.apply(name=name, parentTask=self, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pex_config/14.0-4-gae1598d+1/python/lsst/pex/config/configurableField.py", line 83, in apply
return self.target(*args, config=self.value, **kw)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_algorithms/14.0-19-gbbfecc2c/python/lsst/meas/algorithms/loadIndexedReferenceObjects.py", line 49, in __init__
dataset_config = butler.get("ref_cat_config", name=self.config.ref_dataset_name, immediate=True)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butler.py", line 1412, in get
raise NoResults("No locations for get:", datasetType, dataId)
lsst.daf.persistence.butlerExceptions.NoResults: No locations for get: datasetType:ref_cat_config dataId:DataId(initialdata={'name': 'ps1_pv3_3pi_20170110'}, tag=set())
I searched the forums, but didn’t find anything involving errors with ref_cat_config. Also, when I am running processCcd.py should I only be running it on the object exposures (i.e. exclude the bias/flats/focusing)? Thank you!
You’ll also need the master_schema.fits file (which I think I neglected to mention in the README.txt file).
Can you list the contents of DATA/ref_cats for me (tree -l DATA/refcats)?
See also here for a similar question.
bash-4.2$ tree -l DATA/ref_cats/
DATA/ref_cats/
`-- ps1_pv3_3pi_20170110 -> scam/ps1_pv3_3pi_20170110
0 directories, 1 file
the contents of scam/ps1_pv3_3pi_20170110 are:
bash-4.2$ tree -l scam/ps1_pv3_3pi_20170110/
scam/ps1_pv3_3pi_20170110/
|-- 215042.fits
|-- 215049.fits
|-- 215050.fits
|-- 215051.fits
|-- 215052.fits
|-- 215053.fits
|-- 215055.fits
|-- 226305.fits
|-- 226310.fits
|-- 226318.fits
|-- README.txt
`-- config.py
0 directories, 12 files
Is the master_schema.fits specific to the FITS files chosen, or is it more generic?
I suspect that your link isn’t working. Try ln -s /full/path/to/scam/ps1_pv3_3pi_20170110 DATA/ref_cats, and verify the link with ls -l.
master_schema.fits is an element of the catalog format, so you need it regardless of which shard files you have.
Thank you. Specifying the full path and adding master_schema.fits fixed the ref_cat_config error, though now I am getting an error that processCcd.py is unable to retrieve bias for the given exposures. This is what I am getting:
bash-4.2$ processCcd.py DATA --rerun processCcdOutput --id field=N5846_1
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/processCcd.py'
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/suprimecam/processCcd.py'
CameraMapper INFO: Loading exposure registry from /home/lsst/DATA/registry.sqlite3
CameraMapper INFO: Loading calib registry from /home/lsst/DATA/CALIB/calibRegistry.sqlite3
root INFO: Running: /opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/bin/processCcd.py DATA --rerun processCcdOutput --id field=N5846_1
processCcd INFO: Processing {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}
processCcd.isr INFO: Performing ISR on sensor {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}
daf.persistence.butler INFO: NoResults or IOError (continuing search) while evaluating bypass function for Dataset type:raw_md Data ID:DataId(initialdata={'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}, tag=set()) at location lsst.afw.image.DecoratedImageU at FitsStorage(N5846_1/2009-04-21/01937/W-S-G+/SUPA01090450.fits)
processCcd FATAL: Failed on dataId={'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}: RuntimeError: Unable to retrieve bias for {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}: No registry for lookup
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/ip_isr/14.0-10-g2094653+11/python/lsst/ip/isr/isrTask.py", line 719, in getIsrExposure
exp = dataRef.get(datasetType, immediate=immediate)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butlerSubset.py", line 198, in get
return self.butlerSubset.butler.get(datasetType, self.dataId, **rest)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butler.py", line 1410, in get
location = self._locate(datasetType, dataId, write=False)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butler.py", line 1329, in _locate
location = repoData.repo.map(datasetType, dataId, write=write)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/repository.py", line 246, in map
loc = self._mapper.map(*args, **kwargs)
File "/home/lsst/obs_subaru/python/lsst/obs/suprimecam/suprimecamMapper.py", line 61, in map
return super(SuprimecamMapperBase, self).map(datasetType, copyId, write=write)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/mapper.py", line 166, in map
return func(self.validate(dataId), write)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/obs_base/14.0-28-gd4c92d7+3/python/lsst/obs/base/cameraMapper.py", line 389, in mapClosure
return mapping.map(mapper, dataId, write)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/obs_base/14.0-28-gd4c92d7+3/python/lsst/obs/base/mapping.py", line 466, in map
location = Mapping.map(self, mapper, dataId, write=write)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/obs_base/14.0-28-gd4c92d7+3/python/lsst/obs/base/mapping.py", line 158, in map
actualId = self.need(iter(self.keyDict.keys()), dataId)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/obs_base/14.0-28-gd4c92d7+3/python/lsst/obs/base/mapping.py", line 322, in need
lookups = self.lookup(newProps, newId)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/obs_base/14.0-28-gd4c92d7+3/python/lsst/obs/base/mapping.py", line 512, in lookup
return Mapping.lookup(self, properties, newId)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/obs_base/14.0-28-gd4c92d7+3/python/lsst/obs/base/mapping.py", line 210, in lookup
raise RuntimeError("No registry for lookup")
RuntimeError: No registry for lookup
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 408, in __call__
result = task.run(dataRef, **kwargs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/timer.py", line 150, in wrapper
res = func(self, *args, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/processCcd.py", line 184, in run
exposure = self.isr.runDataRef(sensorRef).exposure
File "/home/lsst/obs_subaru/python/lsst/obs/subaru/isr.py", line 296, in runDataRef
biasExposure = self.getIsrExposure(sensorRef, "bias")
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/ip_isr/14.0-10-g2094653+11/python/lsst/ip/isr/isrTask.py", line 722, in getIsrExposure
raise RuntimeError("Unable to retrieve %s for %s: %s" % (datasetType, dataRef.dataId, exc1))
RuntimeError: Unable to retrieve bias for {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}: No registry for lookup
I’m a bit confused, as contructBias.py and ingestCalibs.py ran fine.
So what’s in the calibration registry? Please post the results of running:
sqlite3 /home/lsst/DATA/CALIB/calibRegistry.sqlite3
.header on
SELECT * FROM bias;
If that’s empty, please post the ingestCalibs.py command you used.
bash-4.2$ sqlite3 /home/lsst/DATA/CALIB/calibRegistry.sqlite3
SQLite version 3.13.0 2016-05-18 10:57:30
Enter ".help" for usage hints.
sqlite> .header on
sqlite> SELECT * FROM bias;
id|filter|ccd|calibDate|validStart|validEnd
1|NONE|0|2009-04-21|2006-07-26|2012-01-16
2|NONE|1|2009-04-21|2006-07-26|2012-01-16
3|NONE|2|2009-04-21|2006-07-26|2012-01-16
4|NONE|3|2009-04-21|2006-07-26|2012-01-16
5|NONE|4|2009-04-21|2006-07-26|2012-01-16
6|NONE|5|2009-04-21|2006-07-26|2012-01-16
7|NONE|6|2009-04-21|2006-07-26|2012-01-16
8|NONE|7|2009-04-21|2006-07-26|2012-01-16
9|NONE|8|2009-04-21|2006-07-26|2012-01-16
10|NONE|9|2009-04-21|2006-07-26|2012-01-16
The ingestCalibs.py command I ran was:
ingestCalibs.py DATA --rerun n5846 --calib /home/lsst/DATA/CALIB --validity 1000 /home/lsst/DATA/rerun/n5846/BIAS/2009-04-21/NONE/BIAS-*.fits
Oh, maybe it’s not related to the calib registry, but pointing to it. Please try:
processCcd.py DATA --calib DATA/CALIB --rerun processCcdOutput --id field=N5846_1
That gives me:
bash-4.2$ processCcd.py DATA --calib DATA/CALIB --rerun processCcdOutput --id field=N5846_1
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/processCcd.py'
root INFO: Loading config overrride file '/home/lsst/obs_subaru/config/suprimecam/processCcd.py'
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/bin/processCcd.py", line 25, in <module>
ProcessCcdTask.parseAndRun()
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 581, in parseAndRun
parsedCmd = argumentParser.parse_args(config=config, args=args, log=log, override=cls.applyOverrides)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/argumentParser.py", line 614, in parse_args
namespace.butler = dafPersist.Butler(inputs=inputs, outputs=outputs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butler.py", line 521, in __init__
self._getCfgs(repoDataList)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/daf_persistence/14.0-17-g2e0c876/python/lsst/daf/persistence/butler.py", line 821, in _getCfgs
cfg, repoData.repoArgs))
RuntimeError: The RepositoryArgs and RepositoryCfg must match for writable repositories, RepositoryCfg:RepositoryCfg(root='/home/lsst/DATA/rerun/processCcdOutput', mapper=<class 'lsst.obs.suprimecam.suprimecamMapper.SuprimecamMapper'>, mapperArgs={}, parents=[RepositoryCfg(root='/home/lsst/DATA', mapper=<class 'lsst.obs.suprimecam.suprimecamMapper.SuprimecamMapper'>, mapperArgs={}, parents=[], policy=None)], policy=None), RepositoryArgs:RepositoryArgs(root='/home/lsst/DATA/rerun/processCcdOutput', cfgRoot=None, mapper=None, mapperArgs={'calibRoot': '/home/lsst/DATA/CALIB'}, tags=set(), mode='rw', policy=None)That’s because the rerun was created with the old (presumably wrong) configuration. Kill it and start over.
rm -r DATA/rerun/processCcdOutput
That worked. Now I am getting:
processCcd FATAL: Failed on dataId={'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 0, 'taiObs': '2009-04-21', 'expTime': 460.0}: ColortermNotFoundError: No colorterm dict found with photoCatName 'ps1_pv3_3pi_20170110'
Traceback (most recent call last):
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/cmdLineTask.py", line 408, in __call__
result = task.run(dataRef, **kwargs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/timer.py", line 150, in wrapper
res = func(self, *args, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/processCcd.py", line 199, in run
icSourceCat=charRes.sourceCat,
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/timer.py", line 150, in wrapper
res = func(self, *args, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/calibrate.py", line 433, in run
icSourceCat=icSourceCat,
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/calibrate.py", line 536, in calibrate
photoRes = self.photoCal.run(exposure, sourceCat=sourceCat, expId=exposureIdInfo.expId)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/timer.py", line 150, in wrapper
res = func(self, *args, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/photoCal.py", line 471, in run
arrays = self.extractMagArrays(matches=matches, filterName=filterName, sourceKeys=sourceKeys)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_base/14.0-6-ge2c9487+58/python/lsst/pipe/base/timer.py", line 150, in wrapper
res = func(self, *args, **keyArgs)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/photoCal.py", line 326, in extractMagArrays
filterName=filterName, photoCatName=self.config.photoCatName, doRaise=True)
File "/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/pipe_tasks/14.0-54-gb4e84373/python/lsst/pipe/tasks/colorterms.py", line 183, in getColorterm
"No colorterm dict found with photoCatName %r" % photoCatName)
lsst.pipe.tasks.colorterms.ColortermNotFoundError: No colorterm dict found with photoCatName 'ps1_pv3_3pi_20170110'
I have added the code from this post to my config/processCcd.py (both the code under LSST-style format and common configuration). More specifically, I added:
config.calibrate.astromRefObjLoader.retarget(LoadIndexedReferenceObjectsTask)
config.calibrate.astromRefObjLoader.ref_dataset_name = "ps1_pv3_3pi_20170110"
config.calibrate.photoRefObjLoader.retarget(LoadIndexedReferenceObjectsTask)
config.calibrate.photoRefObjLoader.ref_dataset_name = "ps1_pv3_3pi_20170110"
config.calibrate.photoCal.photoCatName = "ps1_pv3_3pi_20170110"
and
colorterms = config.calibrate.photoCal.colorterms
from lsst.pipe.tasks.colorterms import ColortermDict, Colorterm
colorterms.data["ps1*"] = ColortermDict(data={
'g': Colorterm(primary="g", secondary="r", c0=-0.00928, c1=-0.0824),
'r': Colorterm(primary="r", secondary="i", c0=-0.00282, c1=-0.0498, c2=-0.0149),
'i': Colorterm(primary="i", secondary="z", c0=0.00186, c1=-0.140, c2=-0.0196),
'z': Colorterm(primary="z", secondary="i", c0=-4.03e-4, c1=0.0967, c2=0.0210),
'B': Colorterm(primary="g", secondary="r", c0=0.02461907, c1=0.20098328, c2=0.00858468),
'V': Colorterm(primary="g", secondary="r", c0=-0.03117934, c1=-0.63134136, c2=0.05056544),
'R': Colorterm(primary="r", secondary="i", c0=-0.01179613, c1=-0.25403307, c2=0.00696479),
'I': Colorterm(primary="i", secondary="r", c0=0.01078282, c1=0.26727768, c2=0.00747123),
})
the latter coming from obs_subaru/config/suprimecam/colorterms.py.
The color terms in obs_subaru/config/suprimecam/colorterms.py are for the SDSS catalog, not PS1.
I think you want to set calibrate.photoCal.applyColorTerms=False to disable the application of color terms.
I am now running into a segmentation fault in processCcd.py. The full error is (apologies for the giant block of text):
processCcd INFO: Processing {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 8, 'taiObs': '2009-04-21', 'expTime': 460.0}
processCcd.isr INFO: Performing ISR on sensor {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 8, 'taiObs': '2009-04-21', 'expTime': 460.0}
daf.persistence.butler INFO: NoResults or IOError (continuing search) while evaluating bypass function for Dataset type:raw_md Data ID:DataId(initialdata={'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 8, 'taiObs': '2009-04-21', 'expTime': 460.0}, tag=set()) at location lsst.afw.image.DecoratedImageU at FitsStorage(N5846_1/2009-04-21/01937/W-S-G+/SUPA01090458.fits)
processCcd.isr.crosstalk INFO: Applying crosstalk corrections to CCD 8 based on Yagi+2012
processCcd.isr INFO: Set 0 BAD pixels to 1855.65
processCcd.isr INFO: Adding a distortion model to the WCS
processCcd.isr INFO: Flattened sky level: 1855.938904 +/- 28.985080
processCcd.isr INFO: Measuring sky levels in 8x16 grids: 1854.532196
processCcd.isr INFO: Sky flatness in 8x16 grids - pp: 0.028817 rms: 0.005004
processCcd.isr INFO: Setting rough magnitude zero point: 35.656895
processCcd.charImage INFO: Processing {'field': 'N5846_1', 'dateObs': '2009-04-21', 'pointing': 1937, 'filter': 'W-S-G+', 'visit': 109045, 'ccd': 8, 'taiObs': '2009-04-21', 'expTime': 460.0}
processCcd.charImage WARN: Source catalog detected and measured with placeholder or default PSF
processCcd.charImage.repair INFO: Identified 1205 cosmic rays.
processCcd.charImage.detection INFO: Detected 1436 positive peaks in 345 footprints and 12 negative peaks in 4 footprints to 50 sigma
processCcd.charImage.detection INFO: Resubtracting the background after object detection
processCcd.charImage.measurement INFO: Measuring 345 sources (345 parents, 0 children)
Caught signal 11, backtrace follows:
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/utils/14.0-10-gaad1ee2+1/lib/libutils.so(+0x15214) [0x7f8d8288f214]
/lib64/libc.so.6(+0x35270) [0x7f8d8bca7270]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(+0xefb08) [0x7f8d1e6f1b08]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(Eigen::internal::general_matrix_matrix_triangular_product<long, double, 1, false, double, 0, false, 0, 2, 0>::run(long, long, double const*, long, double const*, long, double*, long, double const&)+0x430) [0x7f8d1e6f4920]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(lsst::meas::modelfit::Optimizer::_computeDerivatives()+0x1742) [0x7f8d1e6ea5b2]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(lsst::meas::modelfit::Optimizer::_stepImpl(int, lsst::meas::modelfit::OptimizerHistoryRecorder const*, lsst::afw::table::CatalogT<lsst::afw::table::BaseRecord>*)+0x1217) [0x7f8d1e6ef8b7]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(lsst::meas::modelfit::Optimizer::_runImpl(lsst::meas::modelfit::OptimizerHistoryRecorder const*, lsst::afw::table::CatalogT<lsst::afw::table::BaseRecord>*)+0x111) [0x7f8d1e6f06e1]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(+0x53afa) [0x7f8d1e655afa]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(lsst::meas::modelfit::CModelAlgorithm::_applyImpl(lsst::meas::modelfit::CModelResult&, lsst::afw::image::Exposure<float, int, float> const&, lsst::shapelet::MultiShapeletFunction const&, lsst::afw::geom::Point<double, 2> const&, lsst::afw::geom::ellipses::Quadrupole const&, double, double, int) const+0x888) [0x7f8d1e65f648]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/lib/libmeas_modelfit.so(lsst::meas::modelfit::CModelAlgorithm::measure(lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&) const+0x3fb) [0x7f8d1e6602db]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/python/lsst/meas/modelfit/cmodel/cmodel.so(void pybind11::cpp_function::initialize<pybind11::cpp_function::initialize<void, lsst::meas::modelfit::CModelAlgorithm, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(void (lsst::meas::modelfit::CModelAlgorithm::*)(lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&) const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&)#1}, void, lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(pybind11::cpp_function::initialize<void, lsst::meas::modelfit::CModelAlgorithm, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(void (lsst::meas::modelfit::CModelAlgorithm::*)(lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&) const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&)#1}&&, void (*)(lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::operator()(pybind11::detail::function_call) const+0xe2) [0x7f8d166e9ad2]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/python/lsst/meas/modelfit/cmodel/cmodel.so(void pybind11::cpp_function::initialize<pybind11::cpp_function::initialize<void, lsst::meas::modelfit::CModelAlgorithm, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(void (lsst::meas::modelfit::CModelAlgorithm::*)(lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&) const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&)#1}, void, lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(pybind11::cpp_function::initialize<void, lsst::meas::modelfit::CModelAlgorithm, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&, pybind11::name, pybind11::is_method, pybind11::sibling, pybind11::arg, pybind11::arg>(void (lsst::meas::modelfit::CModelAlgorithm::*)(lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&) const, pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&)#1}&&, void (*)(lsst::meas::modelfit::CModelAlgorithm const*, lsst::afw::table::SourceRecord&, lsst::afw::image::Exposure<float, int, float> const&), pybind11::name const&, pybind11::is_method const&, pybind11::sibling const&, pybind11::arg const&, pybind11::arg const&)::{lambda(pybind11::detail::function_call&)#3}::_FUN(pybind11::detail::function_call)+0xe) [0x7f8d166e9c8e]
/opt/lsst/software/stack/stack/miniconda3-4.3.21-10a4fa6/Linux64/meas_modelfit/14.0-3-gda7b0c7+14/python/lsst/meas/modelfit/cmodel/cmodel.so(pybind11::cpp_function::dispatcher(_object*, _object*, _object*)+0xdc6) [0x7f8d166ee0e6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x102) [0x7f8d8cc25302]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyCFunction_FastCallDict+0x102) [0x7f8d8cc25302]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x14895b) [0x7f8d8ccaa95b]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x146514) [0x7f8d8cca8514]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x285) [0x7f8d8cca9515]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x285) [0x7f8d8cca9515]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x10c) [0x7f8d8cca939c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x10c) [0x7f8d8cca939c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148b2a) [0x7f8d8ccaab2a]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148b2a) [0x7f8d8ccaab2a]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x63) [0x7f8d8cca9583]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x9f1a1) [0x7f8d8cc011a1]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148b2a) [0x7f8d8ccaab2a]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
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/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x9f1a1) [0x7f8d8cc011a1]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148b2a) [0x7f8d8ccaab2a]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x63) [0x7f8d8cca9583]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x9f1a1) [0x7f8d8cc011a1]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148b2a) [0x7f8d8ccaab2a]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x31cc) [0x7f8d8ccae2cc]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x63) [0x7f8d8cca9583]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x9f1a1) [0x7f8d8cc011a1]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x10c) [0x7f8d8cca939c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x10c) [0x7f8d8cca939c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3ec9) [0x7f8d8ccaefc9]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x146514) [0x7f8d8cca8514]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x285) [0x7f8d8cca9515]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x285) [0x7f8d8cca9515]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x166) [0x7f8d8cbcdce6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0xcc) [0x7f8d8cbcdf3c]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyObject_Call+0x56) [0x7f8d8cbcdfd6]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0xe444f) [0x7f8d8cc4644f]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x9e) [0x7f8d8cbcdc1e]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x9e) [0x7f8d8cbcdc1e]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x142249) [0x7f8d8cca4249]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0xa520e) [0x7f8d8cc0720e]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0xa5668) [0x7f8d8cc07668]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0xda2ac) [0x7f8d8cc3c2ac]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x9e) [0x7f8d8cbcdc1e]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x9e) [0x7f8d8cbcdc1e]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x14895b) [0x7f8d8ccaa95b]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x146514) [0x7f8d8cca8514]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148c88) [0x7f8d8ccaac88]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x148b2a) [0x7f8d8ccaab2a]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0((null)+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2c40) [0x7f8d8ccadd40]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(+0x147100) [0x7f8d8cca9100]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCodeEx+0x63) [0x7f8d8cca9583]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyEval_EvalCode+0x3b) [0x7f8d8cca95cb]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyRun_FileExFlags+0x130) [0x7f8d8ccdbee0]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(PyRun_SimpleFileExFlags+0x173) [0x7f8d8ccdd4a3]
/opt/lsst/software/stack/python/miniconda3-4.3.21/bin/../lib/libpython3.6m.so.1.0(Py_Main+0xe25) [0x7f8d8ccf88d5]
python(main+0x16d) [0x400c1d]
/lib64/libc.so.6((null)+0xf5) [0x7f8d8bc93c05]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7f8d8bc93c05]
python() [0x4009e9]
Segmentation fault
what’s particularly confusing for me is that the step it crashed on ran fine for 8 prior images, specifically 'ccd': 0-7. I found forum posts stating that most segfaults are due to a mismatch of library versions, so I verified my versions (obs_subaru DM-13148, LSST stack 7-stack-lsst_distrib-w_2018_11).
Most often segfaults are due to mismatched versions, but there are other possibilities. What setup commands have you run, and what packages have you built personally?
Can you run processCcd.py under gdb (e.g., gdb --args $(which python) $(which processCcd.py) ...) and get a backtrace?
I’m not sure what happened, but in the process of making a new docker container with the correct permissions to run gdb, the segfault was fixed and processCcd.py ran all the way through. I assume starting over fixed any library mismatches.